Thanks for posting here, rags1512!
1) All itineraries would be fine. Which is best, depends on your preferences. Here are some considerations. If you want to see more of the country, option A, B or C (entering via Basel) are better, as you'll avoid using the same entrance and departure city. Moreover, the inbound trip from Basel to Interlaken via Thun and Spiez is definitely nice. Now, as for the remaining options: if you're especially interested in scenic views and mountains, I'd prefer A or B, focusing on the Interlaken and Zermatt or the Interlaken and Lucerne regions.
Out of these two, option A including Zermatt requires more traveling time. Did you check the timetable to check such details? Of course that's no problem if you don't mind somewhat longer trips. There's an alternative to plan B, by the way: don't leave from Basel after your stay in Lucerne, but from Geneva, taking the entire Golden Pass train ride down to Montreux first. That too will be a long trip though.
2) Hotels can be found through these accommodation pages:
Once you'e decided on your base towns, you can start looking for hotels through these pages. If you're not able to find anything that suits you, please let us know and provide your specific requirements and budget, so that we provide some tips. Further budget tips are listed at www.myswissalps.com/pl antrip/doityourself/sa vemoney.
3) Whatever option you choose, you'll be traveling extensively during 4 days, so I'd definitely recommend a 4 day Swiss Travel Pass. Please find all details at www.myswissalps.com/sw isstravelpass. The validity section explains where the pass applies. Explanation on the Jungfraujoch is included. Swiss Travel Pass retailers are listed in the price section. Since you're from India, you can order through www.raileurope.co.in and profit from these promo codes.
4) You don't need special winter clothes, as September won't be that cold yet. Do prepare for cold if you visit the Jungfraujoch though. Generally, several layers of clothes, including fleece jackets, will do.